Exact enumeration of three-dimensional lattice proteins

DOI10.1016/J.CPC.2004.09.011zbMATH Open1196.82138DBLPjournals/cphysics/SchiemannBJ05arXivcond-mat/0501401OpenAlexW2119253117WikidataQ61043809 ScholiaQ61043809MaRDI QIDQ709694FDOQ709694

Authors: Reinhard Schiemann, Michael Bachmann, Wolfhard Janke 

Publication date: 18 October 2010

Published in: Computer Physics Communications (Search for Journal in Brave)

Abstract: We present an algorithm for the exhaustive enumeration of all monomer sequences and conformations of short lattice proteins as described by the hydrophobic-polar (HP) model. The algorithm is used for an exact identification of all designing sequences of HP proteins consisting of up to 19 monomers whose conformations are represented by interacting self-avoiding walks on the simple cubic lattice. Employing a parallelized implementation on a Linux cluster, we generate the complete set of contact maps of such walks.

Full work available at URL: https://arxiv.org/abs/cond-mat/0501401

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zbMATH Keywords

polymersself-avoiding walksHP modelcontact mapslattice proteins

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Statistical mechanics of polymers (82D60) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

Cites Work

• Title not available (Why is that?)
• Self-avoiding walks on the simple cubic lattice
• Universal amplitude ratios for three-dimensional self-avoiding walks

Cited In (6)

• Efficient algorithm for computing exact partition functions of lattice polymer models
• A deterministic algorithm for constrained enumeration of transmembrane protein folds
• Parallel algorithm for calculation of the exact partition function of a lattice polymer
• Title not available (Why is that?)
• Exact enumeration of Hamiltonian walks on the \(4\times 4\times 4\) cube and applications to protein folding
• Three-dimensional off-lattice AB model protein with the 89-residue Fibonacci sequence

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